GREENSBORO, N.C.--When you hear the word "bacteria" you might think it's a bad thing. So you get rid of it all - the cleaner the better!

Doctors say this is actually a problem because there are good bacteria out there.

The problem has been growing for decades with a big jump in chronic diseases like Asthma and Diabetes.

Doctors say it's because we're killing off too many good bacteria that could protect us.

Normally, we see germs as a threat. As a society, we've become good at killing the ones that cause infections.

Since the 1950's, the rate of infectious diseases plummeted, but during the same time chronic diseases have skyrocketed.

Is there a link? Are we so obsessed with killing germs that we are making ourselves sick?

According to the National Institutes of Health, Bacteria play a critical role in regulating immunity, metabolism, and other key functions.

Dr. Eric Alm says not all bacteria are bad, but our need to kill germs is giving bad bacteria room to grow.

"Bacteria are pretty exciting they kind of make the world go round in some pretty important ways," Alm explained.

Through studies, scientists have found three things messing with our bodies-- hand sanitizer, allergies, and antibiotics.

A growing number of scientists believe there is a connection between the killing of germs and the rise in chronic diseases.

Now this is where this story takes a wild turn but one scientists made to help find a cure to those chronic diseases.

They're exploring healthy germs living in human waste.

Samples are manipulated and filtered, stored in a deep freeze, and have been implanted in patients with a bacterial disease.

Right now, this treatment is only being used for 'c difficile' - a deadly gastrointestinal infection where antibiotics don't always work.

There are promising trials underway to treat obesity, ulcerative colitis and even autism.

Researchers are trying to isolate the individual bacteria that make this procedure successful… and bottle into a medicine.

So through our research we can conclude that yes, we are so obsessed with being clean we are making ourselves sick.

Parents, doctors say you should let your kids play the in the dirt and with pets because it builds their immune system.

For adults, doctors say veggies might help play a role in developing a strong microbiome which is a build up of micro organisms inside our bodies that help protect us against germs.